Negative ion beam focusing is a key element for advanced applications of negative ion beams such as accelerators for particle physics, compact accelerators for medical fields, and plasma experiments for nuclear fusion because complicated magnetic fields exist both inside of the source plasma and the grid system. In order to understand the beam focusing, phase space structure measurements for a single beamlet have been performed with a research-and-development negative ion source at the National Institute for Fusion Science. A complicated phase space structure is observed in the direction parallel to the filter magnetic field in the vicinity of the plasma grid, while a single-Gaussian beamlet structure is observed in the direction perpendicular to the filter field. Detailed analyses for the phase space structure of the single beamlet reveal that the complicated structure can be identified as a combination of three beam components with different beam axes. The shifts of each axis are also observed to depend on the ratio of the acceleration voltage for the extraction voltage, which may significantly degrade the beamlet focusing.